My Winamp version is 5.04. When I enqueue .apl files which are produced by the MakeAPL utility in Monkey Audio (my version is 3.98), the displayed length of the track in the playlist window is wrong -- an 11-minute song is displayed as lasting 11379 minutes. I don't recall seeing this problem in Winamp before and believe it to be new.

Coding Technologies' .APL extension = aacPlus files.
This is a new supported format in Winamp 5.04
and support is provided by the new aacPlus decoder in in_mp3.dll

You will need to contact the Monkeys Audio people and tell them that their APL extension (APE List file? or whatever it stands for... sorry, I don't use APE) is now in conflict with aacPlus.

Sorry, but there's nothing we can do about it here.

What you can do, is remove APL from the Extension List in the MPEG Audio Decoder config (Prefs > plugins > input > in_mp3.dll > config), which should make in_ape.dll the default handler of Monkeys Audio .APL files again.